Continuity mistake: During the scenes where Pee-Wee is riding with Large Marge, a quick exterior shot of the passenger side of the truck shows Large Marge's rig towing a trailer with horizontal ribbing. After dropping Pee-Wee off at the truck stop, her trailer changes to one with vertical ribbing.
Continuity mistake: When P.W. is escaping certain trouble somehow his handle bar comes off (with ribbons) a new one is replaced (without ribbons) - cool bike huh? But in the next scene the new handle has ribbons... (01:13:00)
Continuity mistake: When Pee Wee gathers everyone together in his basement to discuss his stolen bike, there's a shot of his dog Speck sitting in front of a person wearing horrible plastic pink or orange boots. It's Pee Wee's friend, Dotty. In the next shot, Dotty comes down the stairs... (00:27:05)
Continuity mistake: In the pet store fire scene, you see an aquarium full of fish. At one point Pee Wee stops to rescue them by scooping them into a plastic bag filled with water. While he's doing this, the aquarium is nearly empty. In the last scene of the sequence (as he's running out of the store with the snakes), the aquarium is again chock-full of fish. (01:19:20)
Continuity mistake: When Pee-Wee finds the Alamo, he is shown holding a San Antonio travel brochure. Notice how his right hand grips the bottom near a crease and his left hand holds the left side. In the next shot he lowers the brochure and starts to chuckle out loud, but now his right hand is positioned on the right side instead. (00:52:20)
Continuity mistake: During breakfast, the orange juice container is below the yellow line, then almost full, then later back down again, all while filling with the squeezed orange juice. (00:05:15)
Continuity mistake: As he leaves his house, PeeWee manually turns on his 'sprinklers' (the Water Wiggle toy) and warns his neighbour he is about to start watering the lawn. He then goes to the rear of the property to retrieve his bike. When he returns to the front yard (just a minute or so later) the sprinklers are no longer running. (00:08:05)
Continuity mistake: In the breakfast scene, one shot shows pancake dough being poured onto a frying pan. In next shot, when Pee-Wee goes to the bathroom, the dough is poured again. (00:04:40)
Continuity mistake: When Pee-Wee is walking away from his house with his bike, you can see two lawn gnomes behind him, next to his house. When he sees Francis, the lawn gnomes have mysteriously disappeared.
Continuity mistake: After Pee-Wee loses the Warner Bros. security crew on his tail, he sees a burning pet shop and decides to rescue the animals inside. Take a look at the early '80s red and black Chevy Suburban parked by the entrance. Whenever Pee-Wee runs outside, the amount of sunlight cast on the vehicle changes (sometimes lots of light, very little light or none at all) as though the scene were filmed at different parts of the day, then pieced together. (01:17:25)
Continuity mistake: Early in the Warner Bros. studio chase sequence we see a team of security guards in pursuit of Pee-wee. Somehow the guard in front switches from using a golf cart to a bicycle, all within a few brief cuts. This is the same guard who pulled the right handle from Pee-wee's bike moments ago. (01:13:05)
Continuity mistake: When Pee-Wee is on the roadside trying to hitch a ride to Texas, the sun casts a shadow behind him which is mostly parallel to the road. But in the subsequent shots of oncoming cars, the sun is casting a long shadow on each one's passenger side - obviously implying a different time of day. (00:33:00)